Descrete Events Models + Temporal Logic = Supervisory Controller: Automatic Synthesis of Locomotion Controllers. - Marco Antoniotti; Bud Mishra (ICRA, 1995)

Synthesis and Verification of Controllers for Robotics and Manufacturing Devices with Temporal Logic and the "Control-D" System. - Marco Antoniotti (1995)

SHIFT and SMART-AHS: A Language for Hybrid System Engineering Modeling and Simulation. - Marco Antoniotti; Aleks Göllü (DSL, 1997)

Embedded system design specification: merging reactive control and data computation. - Marco Antoniotti; Alberto Ferrari; Luciano Lavagno; Alberto L. Sangiovanni-Vincentelli; Ellen Sentovich (CDC, 2001)

XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior. - Marco Antoniotti; Alberto Policriti; Nadia Ugel; Bud Mishra (HiPC, 2002)

Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing. - Marco Antoniotti; Bhubaneswar Mishra; Carla Piazza; Alberto Policriti; Marta Simeoni (CMSB, 2003)

Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes. - Marco Antoniotti; F. Park; Alberto Policriti; Nadia Ugel; Bud Mishra (Pacific Symposium on Biocomputing, 2003)

Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice. - Marco Antoniotti; Carla Piazza; Alberto Policriti; Marta Simeoni; Bud Mishra (Theor. Comput. Sci., 2004)

Algorithmic Algebraic Model Checking I: Challenges from Systems Biology. - Carla Piazza; Marco Antoniotti; Venkatesh Mysore; Alberto Policriti; Franz Winkler 001; Bud Mishra (CAV, 2005)

Ontological Modelling for Neurovascular Disease Study: Issues in the Adoption of Description Logic. - Gianluca Colombo; Daniele Merico; Marco Antoniotti; Flavio De Paoli; Giancarlo Mauri (Description Logics, 2007)

Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods. - Italo Zoppis; Daniele Merico; Marco Antoniotti; Bud Mishra; Giancarlo Mauri (ISBRA, 2007)

Evaluating Graph Kernel Methods for Relation Discovery in GO-Annotated Clusters. - Daniele Merico; Italo Zoppis; Marco Antoniotti; Giancarlo Mauri (KES (3), 2007)

From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. - Jomol P. Mathew; Barry S. Taylor; Gary D. Bader; Saiju Pyarajan; Marco Antoniotti; Arul M. Chinnaiyan; Chris Sander; Steven J. Burakoff; Bud Mishra (PLoS Comput. Biol., 2007)

CLAZY: Lazy Calling for Common Lisp. - Marco Antoniotti (ELS, 2008)

Ontological modeling at a domain interface: bridging clinical and biomolecular knowledge. - Gianluca Colombo; Daniele Merico; Zoltán Nagy 004; Flavio De Paoli; Marco Antoniotti; Giancarlo Mauri (Knowl. Eng. Rev., 2009)

Identification of Individualized Feature Combinations for Survival Prediction in Breast Cancer: A Comparison of Machine Learning Techniques. - Leonardo Vanneschi; Antonella Farinaccio; Mario Giacobini; Giancarlo Mauri; Marco Antoniotti; Paolo Provero (EvoBIO, 2010)

An application of kernel methods to gene cluster temporal meta-analysis. - Marco Antoniotti; Marco Carreras; Antonella Farinaccio; Giancarlo Mauri; Daniele Merico; Italo Zoppis (Comput. Oper. Res., 2010)

An ontological modeling approach to cerebrovascular disease studies: The NEUROWEB case. - Gianluca Colombo; Daniele Merico; Giorgio Boncoraglio; Flavio De Paoli; John Ellul; Giuseppe Frisoni; Zoltán Nagy 004; Aad van der Lugt; István Vassányi; Marco Antoniotti (J. Biomed. Informatics, 2010)

A comparison of machine learning techniques for survival prediction in breast cancer. - Leonardo Vanneschi; Antonella Farinaccio; Giancarlo Mauri; Marco Antoniotti; Paolo Provero; Mario Giacobini (BioData Min., 2011)

Analysis of Correlation Structures in Renal Cell Carcinoma Patient Data. - Italo Zoppis; Massimiliano Borsani; Erica Gianazza; Clizia Chinello; Francesco Rocco; Giancarlo Albo; André M. Deelder; Yuri E. M. van der Burgt; Fulvio Magni; Marco Antoniotti; Giancarlo Mauri (BIOINFORMATICS, 2012)

Poster: Characterization of distinguishing regions for Renal Cell Carcinoma discrimination. - Italo Zoppis; Massimiliano Borsani; Erica Gianazza; Clizia Chinello; Giancarlo Albo; Francesco Rocco; André M. Deelder; Yuri E. M. van der Burgt; Marco Antoniotti; Fulvio Magni; Giancarlo Mauri (ICCABS, 2012)

Effects of delayed immune-response in tumor immune-system interplay - Giulio Caravagna; Alex Graudenzi; Marco Antoniotti; Giancarlo Mauri; Alberto d'Onofrio (HSB, 2012)

Self-Stabilization in Membrane Systems. - Marco Antoniotti; Rudolf Freund; Alberto Leporati; Giancarlo Mauri (Comput. Sci. J. Moldova, 2012)

Mutual Information Optimization for Mass Spectra Data Alignment. - Italo Zoppis; Erica Gianazza; Massimiliano Borsani; Clizia Chinello; Veronica Mainini; Carmen Galbusera; Carlo Ferrarese; Gloria Galimberti; Alessandro Sorbi; Barbara Borroni; Fulvio Magni; Marco Antoniotti; et al. (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Copy-Number Alterations for Tumor Progression Inference. - Claudia Cava; Italo Zoppis; Manuela Gariboldi; Isabella Castiglioni; Giancarlo Mauri; Marco Antoniotti (AIME, 2013)

GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. - Marco Antoniotti; Gary D. Bader; Giulio Caravagna; Silvia Crippa; Alex Graudenzi; Giancarlo Mauri (Bioinform., 2013)

Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts. - Giulio Caravagna; Alex Graudenzi; Marco Antoniotti; Giovanni De Matteis (WIVACE, 2013)

A Model of Colonic Crypts using SBML Spatial. - Daniele Ramazzotti; Carlo Maj; Marco Antoniotti (WIVACE, 2013)

Characterizing the computational power of energy-based P systems. - Artiom Alhazov; Marco Antoniotti; Alberto Leporati (Int. J. Comput. Math., 2013)

Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model. - Alex Graudenzi; Chiara Damiani; Andrea Paroni; Alessandro Filisetti; Marco Villani 001; Roberto Serra; Marco Antoniotti (WIVACE, 2014)

Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays. - Giulio Caravagna; Alberto d'Onofrio; Marco Antoniotti; Giancarlo Mauri (Inf. Comput., 2014)

Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference. - Claudia Cava; Italo Zoppis; Manuela Gariboldi; Isabella Castiglioni; Giancarlo Mauri; Marco Antoniotti (J. Clin. Bioinform., 2014)

CAPRI: efficient inference of cancer progression models from cross-sectional data. - Daniele Ramazzotti; Giulio Caravagna; Loes Olde Loohuis; Alex Graudenzi; Ilya Korsunsky; Giancarlo Mauri; Marco Antoniotti; Bud Mishra (Bioinform., 2015)

Automatising the analysis of stochastic biochemical time-series. - Giulio Caravagna; Luca De Sano; Marco Antoniotti (BMC Bioinform., 2015)

Parallel implementation of efficient search schemes for the inference of cancer progression models. - Daniele Ramazzotti; Marco S. Nobile; Paolo Cazzaniga; Giancarlo Mauri; Marco Antoniotti (CIBCB, 2016)

TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. - Luca De Sano; Giulio Caravagna; Daniele Ramazzotti; Alex Graudenzi; Giancarlo Mauri; Bud Mishra; Marco Antoniotti (Bioinform., 2016)

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. - Andrea Paroni; Alex Graudenzi; Giulio Caravagna; Chiara Damiani; Giancarlo Mauri; Marco Antoniotti (BMC Bioinform., 2016)

Modeling cumulative biological phenomena with Suppes-Bayes causal networks. - Daniele Ramazzotti; Alex Graudenzi; Marco Antoniotti (CoRR, 2016)

Ordering cancer mutational profiles of cross-sectional copy number alterations. - Alex Graudenzi; Giulio Caravagna; Iuliana M. Bocicor; Claudia Cava; Marco Antoniotti; Giancarlo Mauri (Int. J. Data Min. Bioinform., 2016)

Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. - Marco Antoniotti; Giulio Caravagna; Luca De Sano; Alex Graudenzi; Giancarlo Mauri; Bud Mishra; Daniele Ramazzotti (R J., 2016)

Learning the Probabilistic Structure of Cumulative Phenomena with Suppes-Bayes Causal Networks. - Daniele Ramazzotti; Marco S. Nobile; Marco Antoniotti; Alex Graudenzi (CoRR, 2017)

Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. - Daniele Ramazzotti; Alex Graudenzi; Luca De Sano; Marco Antoniotti; Giulio Caravagna (CoRR, 2017)

Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena. - Daniele Ramazzotti; Marco S. Nobile; Marco Antoniotti; Alex Graudenzi (ICCS (1), 2018)

Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. - Davide Maspero; Alex Graudenzi; Satwinder Singh; Dario Pescini; Giancarlo Mauri; Marco Antoniotti; Chiara Damiani (WIVACE, 2018)

Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. - Alex Graudenzi; Davide Maspero; Marzia Di Filippo; Marco Gnugnoli; Claudio Isella; Giancarlo Mauri; Enzo Medico; Marco Antoniotti; Chiara Damiani (J. Biomed. Informatics, 2018)

cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models. - Lucrezia Patruno; Edoardo Galimberti; Daniele Ramazzotti; Giulio Caravagna; Luca De Sano; Marco Antoniotti; Alex Graudenzi (CIBB, 2019)

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. - Daniele Ramazzotti; Alex Graudenzi; Luca De Sano; Marco Antoniotti; Giulio Caravagna (BMC Bioinform., 2019)

Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena. - Daniele Ramazzotti; Marco S. Nobile; Marco Antoniotti; Alex Graudenzi (J. Comput. Sci., 2019)

Understanding Deep Learning with Activation Pattern Diagrams. - Francesco Craighero; Alex Graudenzi; Fabrizio Angaroni; Fabio Stella; Marco Antoniotti (XAI.it@AI*IA, 2020)

A closed-loop optimization framework for personalized cancer therapy design. - Fabrizio Angaroni; Mattia Pennati; Lucrezia Patruno; Davide Maspero; Marco Antoniotti; Alex Graudenzi (CIBCB, 2020)

Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp ... or: Hammering Some Sense into : ieee-floating-point. - Marco Antoniotti (ELS, 2020)

On the automatic calibration of fully analogical spiking neuromorphic chips. - Daniele M. Papetti; Simone Spolaor; Daniela Besozzi; Paolo Cazzaniga; Marco Antoniotti; Marco S. Nobile (IJCNN, 2020)

Investigating the Compositional Structure of Deep Neural Networks. - Francesco Craighero; Fabrizio Angaroni; Alex Graudenzi; Fabio Stella; Marco Antoniotti (LOD (1), 2020)

Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp. - Marco Antoniotti (CoRR, 2020)

The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. - Davide Maspero; Chiara Damiani; Marco Antoniotti; Alex Graudenzi; Marzia Di Filippo; Marco Vanoni; Giulio Caravagna; Riccardo Colombo; Daniele Ramazzotti; Dario Pescini (Fundam. Informaticae, 2020)

Optimal Control of a Discrete Time Stochastic Model of an Epidemic Spreading in Arbitrary Networks. - Fabrizio Angaroni; Chiara Damiani; Giulia Ramunni; Marco Antoniotti (ANNSIM, 2021)

EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks. - Francesco Craighero; Fabrizio Angaroni; Fabio Stella; Chiara Damiani; Marco Antoniotti; Alex Graudenzi (CoRR, 2021)

VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. - Daniele Ramazzotti; Fabrizio Angaroni; Davide Maspero; Carlo Gambacorti Passerini; Marco Antoniotti; Alex Graudenzi; Rocco Piazza (Patterns, 2021)

J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. - Fabrizio Angaroni; Alessandro Guidi; Gianluca Ascolani; Alberto d'Onofrio; Marco Antoniotti; Alex Graudenzi (BMC Bioinform., 2022)

LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data. - Daniele Ramazzotti; Fabrizio Angaroni; Davide Maspero; Gianluca Ascolani; Isabella Castiglioni; Rocco Piazza; Marco Antoniotti; Alex Graudenzi (J. Comput. Sci., 2022)

Unity is strength: Improving the detection of adversarial examples with ensemble approaches. - Francesco Craighero; Fabrizio Angaroni; Fabio Stella; Chiara Damiani; Marco Antoniotti; Alex Graudenzi (Neurocomputing, 2023)

A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. - Lucrezia Patruno; Salvatore Milite; Riccardo Bergamin; Nicola Calonaci; Alberto d'Onofrio; Fabio Anselmi; Marco Antoniotti; Alex Graudenzi; Giulio Caravagna (PLoS Comput. Biol., 2023)

LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. - Gianluca Ascolani; Fabrizio Angaroni; Davide Maspero; Francesco Craighero; Narra Lakshmi Sai Bhavesh; Rocco Piazza; Chiara Damiani; Daniele Ramazzotti; Marco Antoniotti; Alex Graudenzi (BMC Bioinform., 2023)